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Marinho ACS, To TT, Darveau RP, Gomes BPFA. Detection and function of lipopolysaccharide and its purified lipid A after treatment with auxiliary chemical substances and calcium hydroxide dressings used in root canal treatment. Int Endod J 2018; 51:1118-1129. [PMID: 29505121 DOI: 10.1111/iej.12920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/27/2018] [Indexed: 02/02/2023]
Abstract
AIM To investigate the influence of auxiliary chemical substances (ACSs) and calcium hydroxide [Ca(OH)2 ] dressings on lipopolysaccharides (LPS)/lipid A detection and its functional ability in activating Toll-like receptor 4 (TLR4). METHODOLOGY Fusobacterium nucleatum pellets were exposed to antimicrobial agents as following: (i) ACS: 5.25%, 2.5% and 1% sodium hypochlorite solutions (NaOCl), 2% chlorhexidine (CHX) (gel and solution) and 17% ethylenediaminetetraacetic acid (EDTA); (ii) intracanal medicament: Ca(OH)2 paste for various periods (1 h, 24 h, 7 days, 14 days and 30 days); (iii) combination of substances: (a) 2.5% NaOCl (1 h), followed by 17% EDTA (3 min) and Ca(OH)2 (7 days); (b) 2% CHX (1 h), afterwards, 17% EDTA (3 min) followed by Ca(OH)2 (7 days). Saline solution was the control. Samples were submitted to LPS isolation and lipid A purification. Lipid A peaks were assessed by matrix-assisted laser desorption ionization time-of-flight mass spectrom (MALDI-TOF MS) whilst LPS bands by SDS-PAGE separation and silver staining. TLR4 activation determined LPS function activities. Statistical comparisons were carried out using one-way anova with Tukey-Kramer post-hoc tests at the 5% significance level. RESULTS Matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of control lipid A demonstrated the ion cluster at mass/charge (m/z) 1882 and an intense band in SDS-PAGE followed by silver staining of control LPS. In parallel, LPS control induced a robust TLR4 activation when compared to ACS (P ≤ .001). 5.25% NaOCl treatment led to the absence of lipid A peaks and LPS bands, whilst no changes occurred to lipid A/LPS after treatment with others ACS. Concomitantly, 5.25% NaOCl-treated LPS did not activate TLR4 (P < .0001). As for Ca(OH)2 , lipid A was not detected by MALDI-TOF nor by gel electrophoresis within 24 h. LPS treated with Ca(OH)2 was a weak TLR4 activator (P < .0001). From 24 h onwards, no significant differences were found amongst the time periods tested (P > 0.05). The addition of Ca(OH)2 for 7 days to cells treated either with 2.5% NaOCl or 2% CHX led to the absence of lipid A peaks and LPS bands, leading to a lower activation of TLR4. CONCLUSION 5.25% NaOCl and Ca(OH)2 dressings from 24 h onwards were able to induce both, loss of lipid A peaks and no detection of LPS bands, rendering a diminished immunostimulatory activity through TLR4.
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Affiliation(s)
- A C S Marinho
- Department of Restorative Dentistry, Endodontics Division, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, SP, Brazil
| | - T T To
- Department of Periodontics, University of Washington School of Dentistry, Seattle, WA, USA
| | - R P Darveau
- Department of Periodontics, University of Washington School of Dentistry, Seattle, WA, USA
| | - B P F A Gomes
- Department of Restorative Dentistry, Endodontics Division, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, SP, Brazil
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Resveratrol Modulation of Protein Expression in parkin-Mutant Human Skin Fibroblasts: A Proteomic Approach. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2198243. [PMID: 29138676 PMCID: PMC5613453 DOI: 10.1155/2017/2198243] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/19/2017] [Indexed: 01/12/2023]
Abstract
In this study, we investigated by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) analysis the effects of resveratrol treatment on skin primary fibroblasts from a healthy subject and from a parkin-mutant early onset Parkinson's disease patient. Parkin, an E3 ubiquitin ligase, is the most frequently mutated gene in hereditary Parkinson's disease. Functional alteration of parkin leads to impairment of the ubiquitin-proteasome system, resulting in the accumulation of misfolded or aggregated proteins accountable for the neurodegenerative process. The identification of proteins differentially expressed revealed that resveratrol treatment can act on deregulated specific biological process and molecular function such as cellular redox balance and protein homeostasis. In particular, resveratrol was highly effective at restoring the heat-shock protein network and the protein degradation systems. Moreover, resveratrol treatment led to a significant increase in GSH level, reduction of GSSG/GSH ratio, and decrease of reduced free thiol content in patient cells compared to normal fibroblasts. Thus, our findings provide an experimental evidence of the beneficial effects by which resveratrol could contribute to preserve the cellular homeostasis in parkin-mutant fibroblasts.
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Kumar M, Singh R, Meena A, Patidar BS, Prasad R, Chhabra SK, Bansal SK. An Improved 2-Dimensional Gel Electrophoresis Method for Resolving Human Erythrocyte Membrane Proteins. PROTEOMICS INSIGHTS 2017; 8:1178641817700880. [PMID: 28469466 PMCID: PMC5398320 DOI: 10.1177/1178641817700880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Abstract
The 2-dimensional gel electrophoresis (2-DE) technique is widely used for the analysis of complex protein mixtures extracted from biological samples. It is one of the most commonly used analytical techniques in proteomics to study qualitative and quantitative protein changes between different states of a cell or an organism (eg, healthy and diseased), conditionally expressed proteins, posttranslational modifications, and so on. The 2-DE technique is used for its unparalleled ability to separate thousands of proteins simultaneously. The resolution of the proteins by 2-DE largely depends on the quality of sample prepared during protein extraction which increases results in terms of reproducibility and minimizes protein modifications that may result in artifactual spots on 2-DE gels. The buffer used for the extraction and solubilization of proteins influences the quality and reproducibility of the resolution of proteins on 2-DE gel. The purification by cleanup kit is another powerful process to prevent horizontal streaking which occurs during isoelectric focusing due to the presence of contaminants such as salts, lipids, nucleic acids, and detergents. Erythrocyte membrane proteins serve as prototypes for multifunctional proteins in various erythroid and nonerythroid cells. In this study, we therefore optimized the selected major conditions of 2-DE for resolving various proteins of human erythrocyte membrane. The modification included the optimization of conditions for sample preparation, cleanup of protein sample, isoelectric focusing, equilibration, and storage of immobilized pH gradient strips, which were further carefully examined to achieve optimum conditions for improving the quality of protein spots on 2-DE gels. The present improved 2-DE analysis method enabled better detection of protein spots with higher quality and reproducibility. Therefore, the conditions established in this study may be used for the 2-DE analysis of erythrocyte membrane proteins for different diseases, which may help to identify the proteins that may serve as markers for diagnostics as well as targets for development of new therapeutic potential.
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Affiliation(s)
- Manoj Kumar
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajendra Singh
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Anil Meena
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Bhagwan S Patidar
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajendra Prasad
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.,A28, Sector 3, Aliganj, Lucknow, UP, India
| | - Sunil K Chhabra
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.,Department of Pulmonary, Sleep and Critical Care Medicine, Primus Super Speciality Hospital, Chanakyapuri, New Delhi, India
| | - Surendra K Bansal
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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Vergara D, Simeone P, Latorre D, Cascione F, Leporatti S, Trerotola M, Giudetti AM, Capobianco L, Lunetti P, Rizzello A, Rinaldi R, Alberti S, Maffia M. Proteomics analysis of E-cadherin knockdown in epithelial breast cancer cells. J Biotechnol 2015; 202:3-11. [DOI: 10.1016/j.jbiotec.2014.10.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/06/2014] [Accepted: 10/14/2014] [Indexed: 12/31/2022]
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Vergara D, Simeone P, del Boccio P, Toto C, Pieragostino D, Tinelli A, Acierno R, Alberti S, Salzet M, Giannelli G, Sacchetta P, Maffia M. Comparative proteome profiling of breast tumor cell lines by gel electrophoresis and mass spectrometry reveals an epithelial mesenchymal transition associated protein signature. MOLECULAR BIOSYSTEMS 2014; 9:1127-38. [PMID: 23247860 DOI: 10.1039/c2mb25401h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The epithelial to mesenchymal transition (EMT) is a cellular program associated with the organ morphogenesis but also with the disease progression. EMT in the cancer field fuels neoplastic progression promoting the resistance to cell death, the resistance to chemotherapy and the acquisition of stem cell properties. Considering the crucial role of EMT in breast cancer metastasis, a better understanding of this process may provide new therapeutic options. Here, by using a proteomic approach we identified a set of proteins differentially expressed between an epithelial and a mesenchymal breast cancer cell line. The protein-protein network of these identified proteins was determined by an in silico analysis highlighting, in the EMT program, the role of proteins involved in cell adhesion, migration, and invasion, together with protein kinases involved in proliferation and survival, with many of these emerging as possible targets of novel biological agents. Finally, the pharmacological inhibition of some of these kinases was able to reverse the mesenchymal phenotype to an epithelial phenotype.
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Affiliation(s)
- Daniele Vergara
- Laboratory of General Physiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 73100, Lecce, Italy
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Abstract
Most biological processes including growth, proliferation, differentiation, and apoptosis are coordinated by tightly regulated signaling pathways, which also involve secreted proteins acting in an autocrine and/or paracrine manner. In addition, extracellular signaling molecules affect local niche biology and influence the cross-talking with the surrounding tissues. The understanding of this molecular language may provide an integrated and broader view of cellular regulatory networks under physiological and pathological conditions. In this context, the profiling at a global level of cell secretomes (i.e., the subpopulations of a proteome secreted from the cell) has become an active area of research. The current interest in secretome research also deals with its high potential for the biomarker discovery and the identification of new targets for therapeutic strategies. Several proteomic and mass spectrometry platforms and methodologies have been applied to secretome profiling of conditioned media of cultured cell lines and primary cells. Nevertheless, the analysis of secreted proteins is still a very challenging task, because of the technical difficulties that may hamper the subsequent mass spectrometry analysis. This chapter describes a typical workflow for the analysis of proteins secreted by cultured cells. Crucial issues related to cell culture conditions for the collection of conditioned media, secretome preparation, and mass spectrometry analysis are discussed. Furthermore, an overview of quantitative LC-MS-based approaches, computational tools for data analysis, and strategies for validation of potential secretome biomarkers is also presented.
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Teles LMB, Aquino EN, Neves ACD, Garcia CHS, Roepstorff P, Fontes B, Castro MS, Fontes W. Comparison of the neutrophil proteome in trauma patients and normal controls. Protein Pept Lett 2012; 19:663-72. [PMID: 22519539 PMCID: PMC3382372 DOI: 10.2174/092986612800493977] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 12/12/2011] [Accepted: 12/14/2011] [Indexed: 01/11/2023]
Abstract
Background: Neutrophils have an impressive array of microbicidal weapons, and in the presence of a pathogen, progress from a quiescent state in the bloodstream to a completely activated state. Failure to regulate this activation, for example, when the blood is flooded with cytokines after severe trauma, causes inappropriate neutrophil activation that paradoxically, is associated with tissue and organ damage. Acidic proteomic maps of quiescent human neutrophils were analyzed and compared to those of activated neutrophils from severe trauma patients. The analysis revealed 114 spots whose measured volumes differed between activated and quiescent neutrophils, with 27 upregulated and 87 downregulated in trauma conditions. Among the identified proteins, grancalcin, S100-A9 and CACNB2 reinforce observed correlations between motility and ion flux, ANXA3, SNAP, FGD1 and Zfyve19 are involved in vesicular transport and exocytosis, and GSTP1, HSPA1 HSPA1L, MAOB, UCH-L5, and PPA1 presented evidence that activated neutrophils may have diminished protection against oxidative damage and are prone to apoptosis. These are discussed, along with proteins involved in cytoskeleton reorganization, reactive oxygen species production, and ion flux. Proteins such as Zfyve19, MAOB and albumin- like protein were described for the first time in the neutrophil. In this work we achieved the identification of several proteins potentially involved in inflammatory signaling after trauma, as well as proteins described for the first time in neutrophils. | ![]() |
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Affiliation(s)
- Liz M B Teles
- Laboratory of Biochemistry and Protein Chemistry, Cell Biology Department, University of Brasília, Brasilia, DF, Brazil. CEP 70910-900
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Burton EO, Hickey WJ. Assessing variability in gel-based proteomic analysis of Nitrosomonas europaea. Methods Enzymol 2011; 496:435-63. [PMID: 21514475 DOI: 10.1016/b978-0-12-386489-5.00018-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Proteomics offers a unique look at the way protein expression changes in response to stimuli, and "gel-based" methods that utilize two-dimensional gel electrophoresis (2-DE) are key technologies in such studies. However, the many steps involved can be technically complex, and the resulting data are subject to variability from both technical and biological sources. Designing 2-DE proteomic studies can be challenging, as a set of standard methods or experimental designs has not been established. This being the case, it is especially important to identify and control sources of variability. Statistically significant results can be obtained if the experimental design includes a sufficient number of replicate 2-DE gels, and if the replicate gels are similar enough to be analyzed in the same experiment. While three or four replicates are often sufficient for compensation of variability, the pilot study illustrated in this chapter showed that statistically significant expression differences could be detected for 90% of the spots matched if six replicate experiments were done.
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Affiliation(s)
- Emily O Burton
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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10
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Cong WT, He HZ, Zhu ZX, Ye CX, Yang XY, Choi JK, Jin LT, Li XK. Improved conditions for silver-ammonia staining of DNA in polyacrylamide gel. Electrophoresis 2010; 31:1662-5. [PMID: 20411569 DOI: 10.1002/elps.200900786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An improved silver-ammonia staining method for DNA on polyacrylamide gels is described. In this method, staining of DNA using silver-ammonia complex allows high sensitivity, low cost, low toxicity, and simple protocol without requiring fixation and sensitization steps. The protocol takes less than 40 min to complete, with a detection limit of 1.5 pg of single DNA band on polyacrylamide gels, approximately 30-fold higher than that of original silver-ammonia staining method. Furthermore, this novel technique not only exhibits high sensitivity for large DNA fragment, but also shows a better trend to detect low-base-pair DNA compared with other silver staining methods.
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Affiliation(s)
- Wei-Tao Cong
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals, Wenzhou Medical College, Wenzhou, Zhejiang, PR China
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CHEN RH, LIU W, ZHANG GS, YE JX. Mitochondrial Proteomic Analysis of Cytoplasmic Male Sterility Line and Its Maintainer in Wheat (Triticum aestivum L.). ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1671-2927(09)60154-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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KÅos P, PorÄba E, Springer E, Lampart-Szczapa E, Józefiak AG. Identification of a Specific IgE-Binding Protein from Narrow-Leafed Lupin (L. Angustifolius) Seeds. J Food Sci 2010; 75:H39-43. [DOI: 10.1111/j.1750-3841.2009.01440.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mandal N, Heegaard S, Prause JU, Honoré B, Vorum H. Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry. Biol Proced Online 2009; 12:56-88. [PMID: 21406065 PMCID: PMC3055252 DOI: 10.1007/s12575-009-9019-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 09/28/2009] [Indexed: 01/30/2023] Open
Abstract
The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.
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Affiliation(s)
- Nakul Mandal
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Steffen Heegaard
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Ulrik Prause
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Bent Honoré
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Henrik Vorum
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
- Department of Ophthalmology, Aalborg Hospital, Aarhus University Hospital, Aalborg, Denmark
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Abstract
Silver staining detects proteins after electrophoretic separation on polyacrylamide gels. Its main positive features are its excellent sensitivity (in the low nanogram range) and the use of very simple and cheap equipment and chemicals. The sequential phases of silver staining are protein fixation, then sensitization, then silver impregnation, and finally image development. Several variants of silver staining are described here, which can be completed in a time range from 2 h to 1 day after the end of the electrophoretic separation. Once completed, the stain is stable for several weeks.
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Villiers C, Chevallet M, Diemer H, Couderc R, Freitas H, Van Dorsselaer A, Marche PN, Rabilloud T. From secretome analysis to immunology: chitosan induces major alterations in the activation of dendritic cells via a TLR4-dependent mechanism. Mol Cell Proteomics 2009; 8:1252-64. [PMID: 19279042 DOI: 10.1074/mcp.m800589-mcp200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dendritic cells are known to be activated by a wide range of microbial products, leading to cytokine production and increased levels of membrane markers such as major histocompatibility complex class II molecules. Such activated dendritic cells possess the capacity to activate naïve T cells. In the present study we demonstrated that immature dendritic cells secrete both the YM1 lectin and lipocalin-2. By testing the ligands of these two proteins, chitosan and siderophores, respectively, we also demonstrated that chitosan, a degradation product of various fungal and protozoal cell walls, induces an activation of dendritic cells at the membrane level, as shown by the up-regulation of membrane proteins such as class II molecules, CD80 and CD86 via a TLR4-dependent mechanism, but is not able to induce cytokine production. This led to the production of activated dendritic cells unable to stimulate T cells. However, costimulation with other microbial products overcame this partial activation and restored the capacity of these activated dendritic cells to stimulate T cells. In addition, successive stimulation with chitosan and then by lipopolysaccharide induced a dose-dependent change in the cytokinic IL-12/IL-10 balance produced by the dendritic cells.
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Affiliation(s)
- Christian Villiers
- double daggerINSERM U823 Analytical Immunology of Chronic Pathologies, Institut Albert Bonniot, BP170, 38042 Grenoble, France and Université Joseph Fourier, F-38041 Grenoble, France
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Chevallet M, Luche S, Diemer H, Strub JM, Van Dorsselaer A, Rabilloud T. Sweet silver: A formaldehyde-free silver staining using aldoses as developing agents, with enhanced compatibility with mass spectrometry. Proteomics 2008; 8:4853-61. [DOI: 10.1002/pmic.200800321] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rabilloud T, Chevallet M, Luche S, Lelong C. Fully denaturing two-dimensional electrophoresis of membrane proteins: A critical update. Proteomics 2008; 8:3965-73. [DOI: 10.1002/pmic.200800043] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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18
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Abstract
An understanding of gene function requires a complementation of gene and gene expression analysis by the systematic analysis of proteins. Progress in plant proteomics has been lagging behind animal and microbial proteomics due to the lack of plant genome data and the problems involved in successful protein extraction from plant material. With the sequencing of more and more plant genomes, this slow progress will soon be overcome. The moss Physcomitrella patens is a model organism in the field of plant functional genomics. P. patens is the first seedless plant for which the complete genome was sequenced. Genome annotation is currently in progress. While identification of proteins requires knowledge of all coding genes of the organism under study, gene annotation and functional characterization benefit greatly from the findings of proteome analysis. The proteome of P. patens is accessible and approaches are under way to increase the spectrum of proteomic methods applied to this plant. Here we provide a protocol for the extraction of proteins from P. patens and describe the basic and still most important method of proteome analysis, two-dimensional polyacrylamide electrophoresis of proteins. As this technique (not entirely unjustifiably) has the reputation of being unpredictably complicated, we provide a detailed protocol intended to reduce the reluctance that many scientists may have in using this technique.
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Affiliation(s)
- Eric Sarnighausen
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
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19
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Abstract
Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It combines excellent sensitivity (in the low nanogram range) with the use of very simple and cheap equipment and chemicals. It is compatible with downstream processing, such as mass spectrometry analysis after protein digestion. The sequential phases of silver staining are protein fixation, then sensitization, then silver impregnation and finally image development. Several variants of silver staining are described here, which can be completed in a time range from 2 h to 1 d after the end of the electrophoretic separation. Once completed, the stain is stable for several weeks.
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Affiliation(s)
- Mireille Chevallet
- Contrôle moléculaire de la réponse immune spécifique
INSERM : U548 CEAUniversité Joseph Fourier - Grenoble I17, Rue Des Martyrs
38054 GRENOBLE CEDEX 9,FR
- Biochimie et biophysique des systèmes intégrés
CNRS : UMR5092 CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble IDBMS/BBSI
17 Rue des martyrs
38054 GRENOBLE CEDEX 9,FR
| | - Sylvie Luche
- Contrôle moléculaire de la réponse immune spécifique
INSERM : U548 CEAUniversité Joseph Fourier - Grenoble I17, Rue Des Martyrs
38054 GRENOBLE CEDEX 9,FR
| | - Thierry Rabilloud
- Contrôle moléculaire de la réponse immune spécifique
INSERM : U548 CEAUniversité Joseph Fourier - Grenoble I17, Rue Des Martyrs
38054 GRENOBLE CEDEX 9,FR
- Biochimie et biophysique des systèmes intégrés
CNRS : UMR5092 CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble IDBMS/BBSI
17 Rue des martyrs
38054 GRENOBLE CEDEX 9,FR
- * Correspondence should be adressed to: Thierry Rabilloud
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Luche S, Lelong C, Diemer H, Van Dorsselaer A, Rabilloud T. Ultrafast coelectrophoretic fluorescent staining of proteins with carbocyanines. Proteomics 2007; 7:3234-44. [PMID: 17849405 DOI: 10.1002/pmic.200700365] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Protein detection on SDS gels or on 2-D gels must combine several features, such as sensitivity, homogeneity from one protein to another, speed, low cost, and user-friendliness. For some applications, it is also interesting to have a nonfixing stain, so that proteins can be mobilized from the gel for further use (electroelution, blotting). We show here that coelectrophoretic staining by fluorophores of the oxacarbocyanine family, and especially diheptyloxacarbocyanine, offers several positive features. The sensitivity is intermediate between the one of colloidal CBB and the one of fluorescent ruthenium complexes. Detection is achieved within 1 h after the end of the electrophoretic process and does not use any fixing or toxic agent. The fluorescent SDS-carbocyanine-protein complexes can be detected either with a laser scanner with an excitation wavelength of 488 nm or with a UV table operating at 302 nm. Excellent sequence coverage in subsequent MS analysis of proteolytic peptides is also achieved with this detection method.
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Affiliation(s)
- Sylvie Luche
- CEA--Laboratoire de Biochimie et Biophysique des systèmes Intégrés, iRTSV/BBSI, CEA-Grenoble, Grenoble, France
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21
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Nebrich G, Herrmann M, Sagi D, Klose J, Giavalisco P. High MS-compatibility of silver nitrate-stained protein spots from 2-DE gels using ZipPlates and AnchorChips for successful protein identification. Electrophoresis 2007; 28:1607-14. [PMID: 17447244 DOI: 10.1002/elps.200600656] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The availability of easy-to-handle, sensitive, and cost-effective protein staining protocols for 2-DE, in conjunction with a high compatibility for subsequent MS analysis, is still a prerequisite for successful proteome research. In this article we describe a quick and easy-to-use methodological protocol based on sensitive, homogeneous, and MS-compatible silver nitrate protein staining, in combination with an in-gel digestion, employing the Millipore 96-well ZipPlate system for peptide preparation. The improved quality and MS compatibility of the generated protein digests, as compared to the otherwise weakly MS-compatible silver nitrate staining, were evaluated on real tissue samples by analyzing 192 Coomassie-stained protein spots against their counterparts from a silver-stained 2-DE gel. Furthermore, the applicability of the experimental setup was evaluated and demonstrated by the analysis of a large-scale MALDI-TOF MS experiment, in which we analyzed an additional ~1000 protein spots from 2-DE gels from mouse liver and mouse brain tissue.
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Affiliation(s)
- Grit Nebrich
- Institute for Human Genetics Humboldt-University Berlin, Charité, Berlin, Germany
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22
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Chevallet M, Diemer H, Van Dorssealer A, Villiers C, Rabilloud T. Toward a better analysis of secreted proteins: the example of the myeloid cells secretome. Proteomics 2007; 7:1757-70. [PMID: 17464941 PMCID: PMC2386146 DOI: 10.1002/pmic.200601024] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The analysis of secreted proteins represents a challenge for current proteomics techniques. Proteins are usually secreted at low concentrations in the culture media, which makes their recovery difficult. In addition, culture media are rich in salts and other compounds interfering with most proteomics techniques, which makes selective precipitation of proteins almost mandatory for a correct subsequent proteomics analysis. Last but not least, the non-secreted proteins liberated in the culture medium upon lysis of a few dead cells heavily contaminate the so-called secreted proteins preparations. Several techniques have been used in the past for concentration of proteins secreted in culture media. These techniques present several drawbacks, such as coprecipitation of salts or poor yields at low protein concentrations. Improved techniques based on carrier-assisted TCA precipitation are described and discussed in this report. These techniques have been used to analyze the secretome of myeloid cells (macrophages, dendritic cells) and enabled to analyze proteins secreted at concentrations close to 1 ng/mL, thereby allowing the detection of some of the cytokines (TNF, IL-12) secreted by the myeloid cells upon activation by bacterial products.
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Affiliation(s)
- Mireille Chevallet
- BBSI, Biochimie et biophysique des systèmes intégrés
CNRS : UMR5092CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble I17 Rue des martyrs
38054 GRENOBLE CEDEX 9,FR
| | - Hélène Diemer
- IPHC, Institut Pluridisciplinaire Hubert Curien
CNRS : UMR7178Université Louis Pasteur - Strasbourg IFR
| | - Alain Van Dorssealer
- IPHC, Institut Pluridisciplinaire Hubert Curien
CNRS : UMR7178Université Louis Pasteur - Strasbourg IFR
| | - Christian Villiers
- Institut d'oncologie/développement Albert Bonniot de Grenoble
INSERM : U823CHU GrenobleEFSUniversité Joseph Fourier - Grenoble IInstitut Albert Bonniot, BP170, 38042 Grenoble Cedex 9,FR
| | - Thierry Rabilloud
- BBSI, Biochimie et biophysique des systèmes intégrés
CNRS : UMR5092CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble I17 Rue des martyrs
38054 GRENOBLE CEDEX 9,FR
- * Correspondence should be adressed to: Thierry Rabilloud
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23
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D'Amici GM, Rinalducci S, Zolla L. Proteomic analysis of RBC membrane protein degradation during blood storage. J Proteome Res 2007; 6:3242-55. [PMID: 17585793 DOI: 10.1021/pr070179d] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Two-dimensional gel electrophoresis and mass spectrometry were used to identify protein profile changes in red blood cell membranes stored over time under atmospheric oxygen, in the presence or absence of protease inhibitors. New spots with lower molecular masses, ranging between 7 and 15 kDa were observed during the first 7 days storage, while over time, further fragments and high-molecular-mass aggregates appeared, seen as a smearing in the upper part of the gel. Some of the protein changes turned out to be shifts in isoelectric point, as a consequence of chemical oxidations. All these new spots were generated as a result of protein attack by reactive oxygen species (ROS). Protein identification revealed that most of the modified proteins are located in the cytoskeleton. During the first 7 days of storage, oxidative degradation was observed prevalently in band 4.2, to a minor extent in bands 4.1 and 3, and in spectrin. After 14 days, there were new fragments from beta-actin, glyceraldehyde-3-phosphate dehydrogenase, band 4.9, and ankyrin, among others. Preliminary protein-protein cross-linked products, involving alpha and beta spectrin, were also detected. The cross-linked products increased over time. Protein degradation was greatly reduced when oxygen was removed and blood was stored under helium. Interestingly, very few spots were related to enzyme activity, and they were more numerous when oxygen was present, suggesting that some proteases may be oxygen-dependent.
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24
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Agnetti G, Kane LA, Guarnieri C, Caldarera CM, Van Eyk JE. Proteomic technologies in the study of kinases: novel tools for the investigation of PKC in the heart. Pharmacol Res 2007; 55:511-22. [PMID: 17548206 PMCID: PMC2693016 DOI: 10.1016/j.phrs.2007.04.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 02/28/2007] [Accepted: 04/16/2007] [Indexed: 01/18/2023]
Abstract
Recent developments in the field of protein separation allows for the analysis of qualitative and quantitative global protein changes in a particular state of a biological system. Due to the enormous number of proteins potentially present in a cell, sub-fractionation and the enrichment of specific organelles are emerging as a necessary step to allow a more comprehensive representation of the protein content. The proteomic studies demonstrate that a key to understand the mechanisms underlying physiological or pathological phenotypes lies, at least in part, in post-translational modifications (PTMs), including phosphorylation of proteins. Rapid improvements in proteomic characterization of amino acid modifications are further expanding our comprehension of the importance of these mechanisms. The present review will provide an overview of technologies available for the study of a proteome, including tools to assess changes in protein quantity (abundance) as well as in quality (PTM forms). Examples of the recent application of these technologies and strategies in the field of kinase signalling will be provided with particular attention on the role of PKC in the heart. Studies of PKC-mediated phosphorylation of cytoskeletal, myofilament and mitochondrial proteins in the heart have provided great insight into the phenotypes of heart failure, hypertrophy and cardioprotection. Proteomics studies of the mitochondria have provided novel evidences for kinase signalling cascades localized to the mitochondria, some of which are known to involve various isoforms of PKC. Proteomics technologies allow for the identification of the different PTM forms of specific proteins and this information is likely to provide insight into the determinants of morphological as well as metabolic mal-adaptations, both in the heart and other tissues.
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25
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:266-277. [PMID: 17262881 DOI: 10.1002/jms.1071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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26
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Miller I, Crawford J, Gianazza E. Protein stains for proteomic applications: which, when, why? Proteomics 2007; 6:5385-408. [PMID: 16991193 DOI: 10.1002/pmic.200600323] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review recollects literature data on sensitivity and dynamic range for the most commonly used colorimetric and fluorescent dyes for general protein staining, and summarizes procedures for the most common PTM-specific detection methods. It also compiles some important points to be considered in imaging and evaluation. In addition to theoretical considerations, examples are provided to illustrate differential staining of specific proteins with different detection methods. This includes a large body of original data on the comparative evaluation of several pre- and post-electrophoresis stains used in parallel on a single specimen, horse serum run in 2-DE (IPG-DALT). A number of proteins/protein spots are found to be over- or under-revealed with some of the staining procedures.
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Affiliation(s)
- Ingrid Miller
- Institut für Medizinische Chemie, Department für Naturwissenschaften, Veterinärmedizinische Universität Wien, Wien, Austria.
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